Genetic Variant MYOSLID-AS1:n.260+25352G>A (chr2-207492268-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000412387.5(MYOSLID-AS1):n.260+25352G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.384 in 146,286 control chromosomes in the GnomAD database, including 14,183 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.38 ( 14183 hom., cov: 29)

Consequence

MYOSLID-AS1
ENST00000412387.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0430

Publications

3 publications found

Variant links:

Genes affected

MYOSLID-AS1 (HGNC:):

MYOSLID-AS1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.435 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
MYOSLID-AS1	ENST00000412387.5 link	n.260+25352G>A	intron_variant	Intron 3 of 4	4
MYOSLID-AS1	ENST00000418850.1 link	n.256+25352G>A	intron_variant	Intron 3 of 5	5
MYOSLID-AS1	ENST00000432413.3 link	n.242+25352G>A	intron_variant	Intron 3 of 5	3

Frequencies

GnomAD3 genomes

AF:

0.384

AC:

56114

AN:

146170

Hom.:

14159

Cov.:

show subpopulations

Gnomad AFR

AF:

0.440

Gnomad AMI

AF:

0.359

Gnomad AMR

AF:

0.438

Gnomad ASJ

AF:

0.335

Gnomad EAS

AF:

0.279

Gnomad SAS

AF:

0.386

Gnomad FIN

AF:

0.375

Gnomad MID

AF:

0.319

Gnomad NFE

AF:

0.350

Gnomad OTH

AF:

0.348

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.384

AC:

56189

AN:

146286

Hom.:

14183

Cov.:

AF XY:

0.388

AC XY:

27637

AN XY:

71306

show subpopulations

African (AFR)

AF:

0.440

AC:

18005

AN:

40924

American (AMR)

AF:

0.438

AC:

6335

AN:

14458

Ashkenazi Jewish (ASJ)

AF:

0.335

AC:

1099

AN:

3284

East Asian (EAS)

AF:

0.279

AC:

1443

AN:

5180

South Asian (SAS)

AF:

0.385

AC:

1817

AN:

4716

European-Finnish (FIN)

AF:

0.375

AC:

3744

AN:

9980

Middle Eastern (MID)

AF:

0.326

AC:

AN:

282

European-Non Finnish (NFE)

AF:

0.350

AC:

22640

AN:

64620

Other (OTH)

AF:

0.356

AC:

711

AN:

1998

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1407

2814

4221

5628

7035

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

504

1008

1512

2016

2520

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.334

Hom.:

6856

Asia WGS

AF:

0.372

AC:

1293

AN:

3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.70

(source)

DANN

Benign

0.72

PhyloP100

0.043

Mutation Taster

=100/0

polymorphism

(source)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over